Methodologies as extracted from the


Prepared by
Lt. Raymond Slagle
George Heimerdinger
NODC/U.S. JGOFS Data Management Office
Woods Hole Oceanographic Institution
Woods Hole, MA 02543
November 1990


(Williams, SIO)
2.1.1 CTD Laboratory Calibrations
2.1.2 Data Acquisition and Display
2.1.3 Post-Acquisition and Post-Cruise Processing Pressure, Temperature, and Salinity Disolved Oxygen Data Additional Processing
(Gardner, TAMU)
(Broenkow, MLML)
2.3.1 Oxygen
2.3.2 Beam attenuation
2.3.3 Fluorescence

2.1 CTD PROFILES (Williams, SIO)

All SIO CTD profiles were taken with a CTD constructed by personnel of the Oceanographic Data Facility (ODF) at SIO, using NBIS Mark IIIB circuit cards, some of which have been modified, together with some cards designed and produced by ODF. Pressure, temperature, conductivity, and oxygen sensors were standard sensors as used in the factory-produced Mark III CTD units. The pressure and oxygen circuit design was not original, however, but was modified to suit ODF data handling and processing philosophies and techniques. The CTD data included one 16-bit and one 8-bit multiplexed channel for the transmission of non-standard parameters, including elapsed time, transmissometer (see Section 2.2), several internal voltages for diagnostic purposes, and rosette-trip confirmation data.

2.1.1 CTD Laboratory Calibrations

Before and after the North Atlantic Bloom Experiment, the CTD pressure and temperature channels were calibrated in the ODF calibration facility. While deep sea reversing thermometers provide some useful information in the event of a detectable change at sea, in general the CTD is more precise than thermometers, and accuracy is enhanced by using high-precision calibration systems ashore. The pressure standard in use at ODF is a Ruska Model 2400 Piston Gage providing pressures accurate to better than 0.01%. The CTD pressure transducer, a Paine Instruments Model 211-35 strain gage, was calibrated at 23 points between 0 and 6100 db, both as pressure was increased and decreased. Its performance was observed at several different temperatures, and to varying maximum pressures, to note the temperature coefficient and the change in hysteresis with depth of cast. Additionally, the transient response of the pressure transducer to temperature changes was observed. The platinum resistance temperature sensor, Rosemount Model 171BJ, was calibrated at several points throughout the temperature range encountered during the expedition, so that temperature could be corrected to within 1 mdeg C. The temperature transfer standard at the ODF calibration facility, a NBIS Model ATB-1250 automatic resistance bridge and Rosemount Model 162CE standard platinum thermometer, is calibrated periodically against several water triple point cells at 0.01 deg C, and a phenoxy-benzene triple point cell at 26.868 deg C. CTD calibrations are performed in the ODF calibration bath, in a 350 liter tank equipped with a Tronac control system. The tank maintains a stability of 0.0002 deg C for as long as is required, and has internal temperature gradients of no more than 1.5 mdeg/meter. It should be clearly noted that the temperatures produced by ODF for this program are on the IPTS-68 temperature scale, rather than the new ITS-90 scale. No laboratory calibrations were performed for either conductivity or oxygen, as it is necessary to collect samples at sea to assure reasonable accuracy from these sensors.

2.1.2 Data Acquisition and Display

CTD data was acquired at a sampling rate of 25 Hz. Raw data was recorded on the audio channel of a video cassette recorder, and in digital form on a hard disk. Data reduction occurred in realtime, converting the 25 Hz data to a 0.5 second time series. During the reduction, the conductivity and pressure channels were lagged by a single pole, low-pass filter to match the response of the temperature sensor, which had a time constant of approximately 500 msec. Individual frames of data were subjected to a filter limiting absolute values and gradients to reasonable and possible values. The data were then averaged into half-second blocks, and the mean and standard deviation of individual points from the mean were calculated. Editing of the data was done with a two-pass standard deviation rejection filter. On the first pass, values exceeding 4 standard devitions from the mean were rejected, and the remaining data were re-averaged. On the second pass, values exceeding 2 standard deviations were rejected, again followed by re-averaging. These half-second blocks of data, with pre-cruise calibration data applied, were displayed on a high-resolution monitor in graphic form during the cast. During each bottle-trip, about 10 seconds of data were averaged to represent the pressure and temperature for the bottle data file.

2.1.3 Post-Acquisition and Post-Cruise Processing

Individual water sample salinities were determined on almost all casts, in sufficient number to closely monitor and correct the EG&G conductivity sensor. After the first few casts, sufficient information was on hand to provide reasonably good realtime corrections, and permit the production of usable shipboard data reports. Dissolved oxygen analyses were performed on many water samples, but no effort was made to process the CTD oxygen sensor data at sea. Following the cruise, the CTD pressure and temperature sensors were completely recalibrated. No significant changes were observed. The pre-cruise and post-cruise calibrations were averaged and used for all casts. The profiles reported here are primarily those taken while lowering the rosette to maximum depth, unless excessive noise or other data problems made the downtrace data unacceptable (a rare occurence in this expedition). This procedure normally provides the cleanest data, avoiding the stops and starts associated with the collection of water samples as the rosette is raised back to the surface. It will be noted that there are occasions where bottle data and CTD data at a given level are different as a result of the different times of data and/or sample collection. Pressure, Temperature, and Salinity

Pressures are considered to be accurate to within 2 db. with a precision of 1 db, cast-to-cast. Correction of the raw data was accomplished with a model of dynamic response of the pressure transducer which takes into consideration pressure error as a function of pressure and dynamically changing temperature, as well as the variable hysteresis of this type of sensor as a function of maximum cast pressure. Temperature accuracy is estimated to be within 0.001 deg C below 10 deg C, and within 0.002 deg C above 10 deg C, with a precision of 0.0005 deg C. The CTD salinities were adjusted to match the bottle salinities unless there was good reason to suspect a particular cast of bottle salinities. Such a reason might be found in the close matching of several CTD potential temperature-salinity diagrams using a constant conductivity correction, when the bottle data suggests changing the CTD conductivity corrections. Both bottle and CTD data were subjected to very close scrutiny following the cruise, to avoid changing CTD data to match bottle data exactly and arbitrarily, when experience demonstrates clearly that bottle salinities are not infallible. In all cases, the conductivity was corrected by adjusting an offset term; there was no change in the slope of conductivity as a simple first-order function of conductivity calculated from bottle salinities and corrected CTD temperatures and pressures. During this expedition, both the salinometer and CTD performed well, and the CTD salinity accuracy is estimated to be the same as the bottle accuracy, within 0.002 psu, with a precision of 0.001 from cast-to-cast. Dissolved Oxygen Data

Dissolved oxygen data were acquired using a Sensormedics (formerly Beckman) dissolved oxygen sensor. CTD downcast raw oxygen current was extracted from the corrected pressure-series data at isopycnals corresponding to the upcast bottle samples. The differences between CTD and bottle oxygens were used on a station-by-station basis to generate coefficients for a sensor model by applying a non-linear fitting procedure. The model includes pressure and temperature effects on sensor membrane permeability. The temperature of the membrane was calculated via low-pass filter from CTD temperature, and used to compute the diffusion time constant for the membrane. CTD pressure, temperature and salinity were lagged to match the O2 response. Oxygen partial pressure was calculated and converted to dissolved oxygen concentration according to Weiss (1970). The oxygen sensor used in the NBIS Mark III CTD is not ideally suited for oceanographic applications in that it consumes both oxygen and itself during the course of measurements, and is therefore inherently unstable over the long term. It often requires several seconds in the water before it is wet enough to respond properly; this is manifested as low oxygen values at the start of some casts. Flow-dependence problems may occur when the lowering rate varies, as at the cast bottom or during bottle trips, where depletion of oxygen at the sensor causes lower oxygen readings. The processed CTDO dissolved oxygen cannot be expected to have the same absolute accuracy throughout the water column as the rosette oxygens, although there have been many instances where individual bottle oxygens have been shown to be in error by the CTD oxygen trace. ODF therefore recommends that investigators use bottle oxygen concentrations for absolute values. However, the continuous oxygen profile is of great value in its detailed structure. Additional Processing

A software filter was used if needed to remove larger conductivity, temperature, or oxygen spiking problems. Less than 0.5% of the time-series data in the very few noisy casts was affected. The downcast portion of each time-series was then reaveraged into 2-decibar pressure intervals. A ship-roll filter was applied to disallow pressure reversals. Density inversions which still remain in high-gradient regions sometimes cannot be accounted for by a mis-match of pressure, temperature and conductivity sensor response. Detailed examination of the raw data typically shows significant mixing occurring in these areas as a consequence of ship roll. The best the ship-roll filter can do is to produce a reduction in the number and/or size of density inversions.


The methods for reducing 25 cm pathlength SeaTech transmissometer data from the JGOFS North Atlantic Bloom Experiment are described below. In addition, these same measurements are discussed in more detail in Gardner et al, (1990). The raw time-series CTD-transmissometer data supplied by SIO ODF group were decimated to one value every 2 decibars using the first value greater than or equal to the even decibar value. The decimated transmissometer data were corrected for aging of the LED light source, index of refraction, temperature and pressure effects using algorithms supplied by SeaTech. The transmissometer voltages were converted to percent transmission. Spikes were removed from the data. Beam attenuation (c) was calculated from the transmission values. The minimum value of (cmin) was subtracted from all c values to yield (cp) (beam attenuation due to particles alone). A linear fit was performed between the cp values and the particle mass concentrations obtained from filtration of water from the Niskin bottles. cp values were adjusted such that a cp of zero yielded a concentration of zero. The equation for conversion is Concentration (ug/l) = 1022 *(cp*g) where g=1 for cp>0.1 and g=square root of (cp/0.1) for cp<0.1 This single equation accounts for a change in the correlation of mass concentration vs. beam attenuation between surface waters and subsurface waters.

2.3 CTD PROFILES - (Broenkow, MLML)

The MLML CTD/Rosette (Yarbrough et al., 1989) was used to make profiles of conductivity, temperature, dissolved oxygen, beam attenuation and in situ fluorescence. Conductivity was measured with a Sea-Bird conductivity cell and MLML pump, temperature with a platinum thermometer (tau = 0.3 sec) and pressure with a Digiquartz transducer. Data were digitized at 0.8 m intervals. Corrections were applied to temperature, salinity, and pressure using laboratory calibrations done before and after the cruise. Pressure corrections for the compressibility of the Sea-Bird cell were applied using the algorithm provided by Sea-Bird Electronics. Corrected data were compared with salinity and temperature field calibration data provided by the Scripps CTD group. Scripps corrected CTD data and ours show excellent agreement. Maximum salinity differences between the SIO and MLML profiles are about +/- 0.02 S.

2.3.1 Oxygen

The oxygen electrode data were obtained with a Beckman polarograph electrode modified at MLML to obtain near-membrane temperatures. The data have been corrected to oxygen concentrations by comparison with titrated calibration samples obtained during ATLANTIS II 119.5. Most of these calibration samples were analyzed by MLML personnel, and the RMS difference with Scripps titrations was 3 umole/kg. Oxygen concentrations were computed from oxygen reduction current via the WHOI algorithm (Owens and Millard, 1984) using near-membrane temperatures and in situ pressure. Corrections for membrane porosity changes may be large, and cynicism is advised when using these data.

2.3.2 Beam Attenuation

The MLML transmissometer is a modified Martek instrument based on the Scripps Visibility Laboratory design (Petzolf and Austin, 1968). Beam attenuation is measured through the folded 1 m path with a Wratten 45 (480 nm) filter and an IR blocking filter. Calibration is done in the laboratory by adjusting instrument gain to a transmission reading of 85.5% in dry air. Drift is estimated aboard ship before and after each cast by diligent cleaning of the windows using alcohol.

2.3.3 Fluorescence

The MLML profiling fluorometer uses Variosens electronics (Frungel and Koch, 1980) and produces log-scaled signals. Excitation is via a Xenon flash lamp and a broad band filter (350-550 nm half power). Fluorescence emission was detected by silicon diode through a 670 nm (half power) long pass filter. These raw data are converted to "rescaled fluorescence" units by comparison with extracted pigment analyses. We provided our own chlorophyll calibrations during ATLANTIS II 119.5 by fluorometric analysis of acetone extracts of water filtered through Whatman GF/F (0.7 micron) filters. The "rescaled fluorescence" units are numerically equivalent to chlorophyll-a concentrations in ug/liter. The term "rescaled fluorescence" is used to acknowledge the fact that fluorescence and chlorophyll concentrations may not covary because of variation in quantum yield. The RMS difference between "rescaled fluorescence" and extracted chlorophyll was 0.27 ug/liter.